J.P.
I would say it is because Daddy is gone so long at a time. My son gets very upset when I work overtime or anything, because he loses out on his time with me. It is probably kind of upsetting to her (though she is probably used to it) that Daddy is sometimes there for bedtime and waking up in the morning, and sometimes he's gone for a while. So when he is there, she is probably afraid he will leave her again. Thats a pretty normal thing for a toddler. Just make sure she gets plenty of time with him when he is around, and as she gets older explain that Daddy has to go to work, but he will always come back home. She will get used to it, but still will probably be so excited to have him the days he is there, that she will want him to take care of her, because she will know he is leaving again and won't be there. It is hard as the mother to see that... but I don't think there is too much you can do about it for right now. She will begin to understand as she gets older. My son is a mommy's boy for sure, but I am also a single mom and he doesn't know his dad. Even though I always come back to pick him up at daycare, and rarely leave him other than that, he is always scared if I leave him at grandma's house, or anyone elses, that mommy won't come back. Even at 2 1/2, he gets worried sometimes. I have never left him overnight, but sometimes he will go to sleep with my mom and I pick him up during the night, but the idea of even going in my mom's room scares him when I am around, he is afraid that if he goes in there or goes to sleep there, I will leave. We were helping her get ready to move today, and were there at naptime, I had to leave and have her put him to sleep because otherwise he would just scream because mommy was leaving him there. As soon as I am gone... he doesn't care anymore. They will outgrow it! Good luck!
J.